musubix3 0.1.4 → 0.1.6

package/.github/plugin/marketplace.json

@@ -3,13 +3,13 @@
   "owner": { "name": "nahisaho" },
   "metadata": {
     "description": "GitHub Copilot CLI specification-driven development skills",
-    "version": "0.1.4"
+    "version": "0.1.6"
   },
   "plugins": [
     {
       "name": "musubix3",
       "source": ".",
-      "version": "0.1.4",
+      "version": "0.1.6",
       "description": "Evidence-driven SDD without duplicating native Copilot capabilities."
     }
   ]

package/.github/skills/sdd-change/SKILL.md

@@ -1,18 +1,20 @@
 ---
 name: sdd-change
-description: "Use for feature additions, behavior changes, bug fixes, refactoring with observable impact, or any request that must propagate through requirements, design, code, tests, traceability, and quality evidence. 機能追加・仕様変更・バグ修正を一貫して反映するときに使用。"
+description: "Use as the MANDATORY first Skill for requests to develop, build, create, implement, add, change, or fix software, including 「開発」「作成」「実装」. Start requirements and design before code, then propagate through tests, traceability, and quality evidence. ソフトウェア開発依頼では実装前に必ず要求定義・設計から開始。"
 ---
 # Integrated change workflow / 統合変更ワークフロー
-Follow the user's input language (日本語 / English). Use Copilot's native
-planning, editing, research, review, security review and subagents where useful.
-This skill coordinates SDD artifacts and checks; it is not another agent runtime.
+Mandatory entrypoint: never start implementation for a natural-language development request before eliciting and validating requirements and design; skip only for explicitly requested implementation of verified, approved artifacts.
+Follow the user's input language. Use native Copilot planning, editing, research, review, security review and subagents.
 Record exactly one final invocation outcome with `npx musubix3 workflow-record
 sdd-change complete --status <status>`; `change-record` separately proves phases.
-Run `workflow-sanitize <copilot.jsonl> <safe.jsonl>` before review when needed,
-then `workflow-verify <safe.jsonl>`; sanitization strictly validates the source.
-For strict evidence, set an expected UUID or pass `--strict --session-id <uuid>`;
-this checks lifecycles; GitHub origin needs strict OIDC with key-bound claims.
+Run `workflow-sanitize <copilot.jsonl> <safe.jsonl>` before review, then
+`workflow-verify <safe.jsonl>`; it validates source-order lifecycles without
+assuming globally monotonic clocks unless `maxEventSkewMs` is explicitly set.
+For large logs, baseline-protect transcript total/line byte limits; never truncate or edit to bypass them.
+For strict evidence, bind an expected UUID; GitHub origin needs strict OIDC.
 Never record multiple declarations per invocation; use only the configured CLI.
+For broad work, use short stages: initialize, requirements, design, real Red,
+Green, integration, trace/formal, quality. Report each result before the next prompt.
 For a staged change, run `change-record <CHANGE-ID> <phase> --requirement
 <REQ-ID...>` after each phase in this exact order: `impact`, `requirements`,
 `design`, `red`, `implementation`, `green`, `quality`.
@@ -27,8 +29,7 @@ Persisted monotonic order, not wall-clock time, proves these phase boundaries.
 2. Read the constitution and relevant requirements, designs, ADRs, code and tests.
 3. Run `npx musubix3 trace impact <id-or-path> --json` and, when code exists,
    `graph index` plus `graph impact <symbol-or-path> --json`.
-4. Separate confirmed intent, assumptions and open questions. Ask only questions
-   that materially affect observable behavior, safety or compatibility.
+4. Separate confirmed intent, assumptions and open questions. When material context is missing, ask exactly one highest-priority question, wait for its answer, then repeat; never batch questions or finalize requirements, design or code while blockers remain.
 
 ## 2. Update specifications first / 仕様を先に更新
 1. For new or changed observable behavior, add or revise EARS requirements and
@@ -60,10 +61,8 @@ Persisted monotonic order, not wall-clock time, proves these phase boundaries.
    `@verifies` annotations in the authoritative implementation and test files.
    Never create proxy or placeholder source files solely to satisfy trace coverage.
    Links are evidence locations, not proof by themselves.
-5. Run focused tests during implementation, then the configured typecheck,
-   build and complete test commands.
-Documentation, formatting and prototypes may omit TDD unless policy requires it;
-record the reason and never exempt observable behavior changes.
+5. Run focused tests, then configured typecheck, build and complete test commands.
+Documentation/prototypes may omit TDD only when policy allows; record the reason.
 ## 4. Rebuild evidence and finish / 根拠更新と完了
 1. Run `trace build`, `trace check --strict`, `graph index`, and `graph gate`.
 2. Run `formal check` when changed requirements fit its documented abstraction;

package/.github/skills/sdd-implementation/SKILL.md

@@ -12,8 +12,11 @@ named npm packages; report a blocker if the executable is unavailable.
 After the work, run `npx musubix3 workflow-record sdd-implementation complete
 --status completed` exactly once.
 
-1. Read the approved requirement/design IDs and constitution. Use native planning
-   for small verifiable changes. Use native subagents only for independent work.
+1. Before editing implementation code, verify that approved requirements and
+   design artifacts exist and both validators pass. If either is absent or invalid,
+   stop and return to `sdd-change`, invoking `sdd-requirements` and `sdd-design`
+   as needed. Do not infer approval from a natural-language request such as
+   "develop", "build", 「開発」, 「作成」, or 「実装」.
 2. For behavior changes and bug fixes, write a meaningful failing test before
    implementation. Configure the selected command with `tddArgs` containing
    `{testId}` or `{testPath}` and a `tddReport`, or use a built-in runner adapter.
@@ -46,7 +49,8 @@ After the work, run `npx musubix3 workflow-record sdd-implementation complete
    ```
    IDs are globally unique. Multiple targets are comma/space-separated.
    Put annotations in the authoritative source and test files, including
-   supported non-JS/TS files; never add a proxy file just to increase coverage.
+   supported non-JS/TS files. In Python, use consecutive `#` comment lines;
+   annotations inside docstrings are ignored and diagnosed. Never add a proxy file just to increase coverage.
    An annotation establishes a link, not proof that code or tests are correct.
 5. Before recording Red, run every configured `tdd.redPreflightCommands`
    formatter/check and let musubix3 enforce that preflight. Then run the
@@ -56,7 +60,9 @@ After the work, run `npx musubix3 workflow-record sdd-implementation complete
    test linkage, source/test SHA-256, operator/location, and killed status.
    Never fabricate results or add a large mutation dependency. Use
    `npx musubix3 mutation doctor --json` to inspect locally available engines
-   and configuration recommendations.
+   and configuration recommendations. Before Python mutation runs, remove
+   existing `__pycache__` directories, then use `-B` for mutation and test
+   commands so stale bytecode is absent and no new `.pyc` files are created.
 6. Regenerate `npx musubix3 trace build`, check `trace check --strict`, then
    `npx musubix3 gate --changed`. Configure real command/argument arrays first.
 7. Use Copilot's native review and security-review capabilities when appropriate.

package/.github/skills/sdd-quality/SKILL.md

@@ -61,7 +61,7 @@ completed` exactly once.
    identities bound to must functional requirements, current source/test
    fingerprints, operator/location, authoritative tests, and killed results.
    Reject survived, skipped, duplicate, conflicting, stale, or unlinked mutants.
-   Run `mutation doctor` for language-aware local probes and remediation;
+   Treat zero executed or non-passing tests as incomplete evidence after exit zero; run `mutation doctor`;
    musubix3 validates evidence and does not bundle a mutation engine.
    Missing required tools, commands, artifacts or evidence block readiness.
 5. Use native review/security-review as needed, recording their findings

package/.github/skills/sdd-requirements/SKILL.md

@@ -13,7 +13,10 @@ After the work, run `npx musubix3 workflow-record sdd-requirements complete
 1. Inspect `.musubix/constitution.md` and the feature's existing requirements.
    If absent, preview `npx musubix3 init --dry-run` before installing.
 2. Use native planning to clarify scope, stakeholders, measurable acceptance and
-   failure behavior. Separate assumptions from confirmed requirements.
+   failure behavior. Separate assumptions from confirmed requirements. If required
+   context is missing, use native elicitation to ask exactly one highest-priority
+   question and wait for the answer before asking the next. Never batch questions.
+   Repeat until no material blocker remains; do not finalize requirements earlier.
 3. Edit `.musubix/features/<slug>/requirements.md` with headings
    `## REQ-FEATURE-001: Title`, `Priority: must|should|may`,
    `Type: functional|non-functional`, and `Statement: ...`. IDs are globally

package/CHANGELOG.md

@@ -2,6 +2,39 @@
 
 ## Unreleased
 
+## 0.1.6 - 2026-09-08
+
+- Make `sdd-change` the mandatory first Skill for natural-language software
+  development requests, elicit missing context one question at a time, and
+  require validated requirements and design before implementation may edit code.
+- Parse Surefire/Failsafe `<testcase>` elements correctly when a self-closing
+  entry precedes one with `<system-out>`/`<system-err>` children, so JUnit
+  identities are no longer dropped or given a neighbouring test's status.
+- Stop counting Java, Kotlin and Scala annotations as calls in Code Graph.
+- Report the offending field and mutant index for invalid schema-v1 mutation
+  reports instead of a single opaque message.
+- Explain that superseded TDD cycles are still validated and must be archived
+  and regenerated rather than replaced by a newer recording.
+- Label `status` artifact counts as requirement and design files, and document
+  the `musubix3/analysis` entry point for `mutationIdentity` plus the
+  `.musubix/evidence/native/` location for command-generated reports.
+- Name the configuration key that raises a rejected workflow transcript total or
+  line size limit instead of only reporting the exceeded bound.
+
+## 0.1.5 - 2026-09-08
+
+- Accept causally ordered concurrent workflow events whose clocks are not
+  monotonic by default, while preserving optional policy-bound timestamp skew.
+- Add policy-protected `workflow.maxTranscriptBytes` and
+  `workflow.maxTranscriptLineBytes` so streaming sanitization and verification
+  can process large real Copilot transcripts without removing resource bounds.
+- Fail structured required test commands that report zero executed tests or
+  skipped tests even when the process exits successfully.
+- Diagnose Python trace annotations hidden in docstrings and recommend
+  bytecode-free Python mutation/test execution to prevent stale `.pyc` results.
+- Guide broad SDD changes through short reviewable stages rather than requiring
+  a single all-inclusive prompt.
+
 ## 0.1.4 - 2026-09-08
 
 - Measure subprocess durations with a monotonic clock and reject negative or

package/README-ja.md

@@ -159,8 +159,13 @@ Copilot の提案を記号的検査で制約する構成であり、独自の「
 
 ## 開発ワークフロー
 
-通常の機能追加、仕様変更、バグ修正には `sdd-change` を使用します。
-以下の全工程を統合し、要求・設計・追跡情報が古いままの実装変更を完了扱いにしません。
+「○○を開発・作成・実装」のような自然言語依頼では、`sdd-change`を必須の
+最初のSkillとして発火させ、コード実装前に要求を確認・検証して設計を確定します。
+承認済みの要求・設計を実装する明示的な依頼だけが`sdd-implementation`へ直接進めます。
+要求または設計が存在しない、あるいは検証に失敗する場合、実装Skillは停止します。
+要求に必要なコンテキストが不足している場合は、優先度が最も高い質問を1問だけ行い、
+回答を待ってから次の1問へ進みます。質問をまとめず、未解決事項がなくなるまで
+要求を確定しません。
 
 1. ネイティブ計画・調査で意図と測定可能な受入条件を明確化。
 2. `change-record CHANGE-ID impact` を記録してから要求を編集・検証し、
@@ -326,6 +331,8 @@ JS/TSはparser-awareなcomment位置を使い、Haskellは`--`と`{- ... -}`、
 Luaは`--`と`--[[ ... ]]`、Visual Basicは`'''` XML documentを含む
 apostrophe commentを扱います。これらは文字列中の記載をリンクとして扱いません。
 その他の言語では対応する行commentまたはblock commentを使用します。
+Pythonは連続した`#` commentを使用してください。docstring内のannotationは無視され、
+`TRACE_ANNOTATION_IN_PYTHON_DOCSTRING`で配置変更を案内します。
 網羅率だけを満たす代理JS/TSファイルは作成しません。
 
 ```ts
@@ -393,7 +400,9 @@ version: 1.0.0
     "mode": "compatible",
     "maxAgeSeconds": 3600,
     "maxFutureSkewSeconds": 60,
-    "maxEventSkewMs": 1000
+    "maxEventSkewMs": 1000,
+    "maxTranscriptBytes": 250000000,
+    "maxTranscriptLineBytes": 2000000
   },
   "attestation": {
     "mode": "local",
@@ -420,8 +429,9 @@ glob は `*` / `**` / `?` に対応し、外部依存は `npm:` 接頭辞で表
 含む完全なrelease checkを要求します。不足設定や弱い設定を証拠で補ったことにはしません。
 `tdd.redPreflightCommands`にはformatter等のplain command名を指定でき、
 Redのtest fingerprintを取得する前に成功が必須です。
-通常ファイルの`pyvenv.cfg`を含む`.venv`と`venv`はsnapshotと
-Code Graphから除外されます。Gradle `.gradle/`、Dart `.dart_tool/`、
+通常ファイルの`pyvenv.cfg`を含む`.venv`と`venv`に加え、生成された
+`__pycache__/` directoryはsnapshotとCode Graphから除外されます。
+sourceなしで実行可能な`.pyc`/`.pyo`単体fileは追跡対象のままです。Gradle `.gradle/`、Dart `.dart_tool/`、
 SwiftPM `.build/`、Zig `.zig-cache/`/`zig-out/`、.NET `.dotnet/`は、
 親directoryに対応manifestがある場合だけ除外されます。同名の任意source
 directoryは追跡対象のままです。
@@ -454,7 +464,9 @@ strict OIDC identity/key binding、必須コマンド名の最低条件です。
 介さず、時間と出力サイズを制限して実コマンドを動かします。個別の必須コマンドは
 集約 `commands` の設定に関係なく失敗・未実行で準備不可になります。
 任意コマンドの失敗は非阻止ですが、憲章が失敗件数を制限していれば不合格です。
-コマンド未設定は skipped です。
+コマンド未設定は skipped です。構造化test commandはprocessがexit 0でも、
+実行testが0件、またはskipped・failed・error testを1件でも報告した場合は
+失敗します。integration suiteが依存service不在のまま暗黙に通ることを防ぎます。
 
 TDD用コマンドには明示的な`tddArgs`と`tddReport`、または組込みの
 `vitest`、`jest`、`pytest`、`go-test`、`cargo`、`junit`、`dotnet` adapterが必要です。
@@ -463,6 +475,8 @@ Vitest/Jestの無関係なskipped結果は対象TDDから除外します。pytes
 `test_TEST_APP_001`形式、Goには`TEST-*`名のsubtest、Cargoには`test_app_001`形式、
 JUnitには正確な`@Tag("TEST-APP-001")`と、IDを含むmethod名または`@DisplayName`を推奨します。
 正規化処理はtestcase属性とJUnit Platformのdisplay-name出力の両方を読み取り、
+Surefire/Failsafeのtestcase要素は自己終了形でも`<system-out>`/`<system-err>`を
+含む形でも解析するため、Spring Bootのbanner等のlog出力で合格IDが欠落しません。
 xUnitには`[Fact(DisplayName = "TEST-APP-001 ...")]`が必要です。
 それぞれXMLまたはTRX report directoryを読み取ります。各フェーズ前に旧レポートを削除し、
 必要なreport親directoryを作成して、対象テストだけを含むfreshな `musubix-json` を要求します。Redは `failed`、
@@ -512,6 +526,9 @@ freshなschema-v1 mutantは、決定的`MUT-<hash>` identity、must functional r
 設定driftを拒否します。既定の`compatible`は証拠なしを許容し、releaseでは`strict`と
 mutation commandをpolicy baselineで保護します。大規模mutation engineは同梱しません。
 mutation/model-correspondenceのsemantic headはattestationに含まれ、元のprovenanceも再検査されます。
+Pythonではstaleな`.pyc`によるfalse survivorを防ぐため、`mutation doctor`は
+各run前の`__pycache__`削除と、その後の`python -B -m mutmut`および
+`python -B -m pytest`を推奨します。
 
 品質根拠は状態、必須フラグ、終了コード・出力、実測値、日時、入力の指紋を保存します。
 変更ゲートのパス、HEAD、影響範囲は後続の通常ゲートでも保持します。
@@ -530,12 +547,20 @@ event数、terminal時刻、raw source hash、canonical transcript hashを保存
 `workflow.expectedSessionId`または`--session-id`でcaller申告sessionの置換を拒否します。
 strict検証は`workflow.maxAgeSeconds`と`workflow.maxFutureSkewSeconds`で
 terminal transcriptの古さと未来方向clock skewも制限します。
-並行eventはtimestamp順で出力されない場合があるため、全体sortではなくtool/resultの
-因果順序を検査します。
+並行eventや異なる実行clockのtimestampは単調にならない場合があるため、JSONLの
+source順でtool/resultの因果関係を検査し、timestamp sortは行いません。
+pair/terminalのclock skewは`maxEventSkewMs`を明示した場合だけ制限し、
+terminalの古さ・未来skew policyは独立して検査します。検証はstreamingかつresource-boundで、
+既定上限は100,000,000 bytesです。大きな実transcriptには`workflow.maxTranscriptBytes`を
+最大1,000,000,000 bytesまで明示設定できます。1 JSONL行は既定1,000,000 bytesで、
+`workflow.maxTranscriptLineBytes`により最大10,000,000 bytesまで設定できます。
+選択した両上限はpolicy baselineで保護できます。
 gate実行中に入力が変わった場合、`input-stability`は追加・変更・削除された各pathと
 前後のSHA-256を報告します。Cargo/Mavenの標準`target/`、manifest直下の
 .NET `bin/`と`obj/`、project-local `.nuget/packages/`は除外しますが、
-source相当の生成入力はfail-closedのままです。組込みadapterは対象test選択とreport引数を
+source相当の生成入力はfail-closedのままです。コマンドが生成するreportは
+追跡対象のsource treeではなく`.musubix/evidence/native/`配下へ出力してください。
+gate中に自身のreportを書き込むとinput stabilityが失敗します。組込みadapterは対象test選択とreport引数を
 所有します。Cargo/Goの既存設定にある先頭`test`は安全に統合し、
 `--json-report`など競合するreport引数は早期拒否します。
 実行中の入力変更は失敗、その後の変更は `status` で stale になります。

package/README.md

@@ -162,9 +162,14 @@ no separate “neurosymbolic AI” model or claims of learned verification.
 
 ## Workflow
 
-For normal feature additions, behavior changes and bug fixes, use `sdd-change`.
-It coordinates the complete workflow below and refuses to call an
-implementation-only change complete while required artifacts remain stale.
+Natural-language requests such as “develop/build/create/implement X” activate
+`sdd-change` as the mandatory first Skill. It elicits and validates requirements
+and design before implementation; only an explicit request to implement existing
+approved artifacts may enter `sdd-implementation` directly. The implementation
+Skill fails closed when those validated artifacts are absent or invalid. When
+material context is missing, requirements elicitation asks one highest-priority
+question at a time and waits for the answer; it does not batch questions or
+finalize requirements while blockers remain.
 
 1. Use native planning/research to establish intent and measurable acceptance.
 2. Record `change-record CHANGE-ID impact`, then edit/validate requirements and
@@ -324,7 +329,9 @@ Source/test trace annotations are read from language comments. JS/TS uses
 parser-aware comment locations; Haskell supports `--` and `{- ... -}`, Lua
 supports `--` and `--[[ ... ]]`, and Visual Basic supports apostrophe comments
 including `'''` XML documentation. These scanners exclude string literals;
-other languages require their supported line or block comments:
+other languages require their supported line or block comments. Python annotations
+must use consecutive `#` comments; annotation-like text in docstrings is ignored
+with `TRACE_ANNOTATION_IN_PYTHON_DOCSTRING` guidance:
 
 ```ts
 /** @id CODE-AUTH-001
@@ -393,7 +400,9 @@ Example `.musubix/config.json` (adapt command arguments to your own project):
     "mode": "compatible",
     "maxAgeSeconds": 3600,
     "maxFutureSkewSeconds": 60,
-    "maxEventSkewMs": 1000
+    "maxEventSkewMs": 1000,
+    "maxTranscriptBytes": 250000000,
+    "maxTranscriptLineBytes": 2000000
   },
   "attestation": {
     "mode": "local",
@@ -422,7 +431,9 @@ or weakened settings rather than silently filling in evidence.
 Use `tdd.redPreflightCommands` to reference plain configured formatter commands;
 they must pass before Red captures the authoritative test fingerprint.
 Conventional `.venv` and `venv` Python environments containing a regular
-`pyvenv.cfg` are excluded from source snapshots and Code Graph indexing.
+`pyvenv.cfg`, plus generated `__pycache__/` directories, are excluded from
+source snapshots and Code Graph indexing. Standalone `.pyc`/`.pyo` files remain
+tracked because Python can execute source-less bytecode modules.
 Gradle `.gradle/`, Dart `.dart_tool/`, SwiftPM `.build/`, Zig
 `.zig-cache/`/`zig-out/`, and .NET `.dotnet/` CLI homes are excluded only when
 their parent contains the corresponding project manifest. Arbitrary same-named
@@ -459,8 +470,11 @@ requires independent approval. Protect the baseline with review/CODEOWNERS.
 **Only run trusted configuration**: gates execute its commands with inherited
 environment, no shell interpretation and bounded time/output. Required command
 failure or skip blocks readiness regardless of `requiredChecks.commands`.
-Optional command failures are nonblocking unless a constitution rule rejects the
-measured count. No configured commands is skipped, not passed.
+A structured test command also fails if it reports no executed tests or any
+skipped, failed, or errored test, even when its process exits zero; this prevents integration suites
+from silently passing without their dependencies. Optional command failures are
+nonblocking unless a constitution rule rejects the measured count. No configured
+commands is skipped, not passed.
 TDD commands require either command-specific `tddArgs` plus a `tddReport`, or a
 built-in `vitest`, `jest`, `pytest`, `go-test`, `cargo`, `junit`, or `dotnet` adapter.
 Explicit custom configuration takes precedence. Adapters derive targeted
@@ -471,6 +485,9 @@ names such as `test_TEST_APP_001`. Go uses a `TEST-*` subtest name, Cargo uses a
 Rust identifier such as `test_app_001`. JUnit methods should carry an exact
 `@Tag("TEST-APP-001")` and an ID-bearing method name or `@DisplayName`; the
 normalizer reads both testcase attributes and JUnit Platform display-name output.
+Surefire/Failsafe testcase elements are parsed whether they are self-closing or
+carry `<system-out>`/`<system-err>` children, so framework logging such as the
+Spring Boot banner does not hide passing identities.
 xUnit tests use
 `[Fact(DisplayName = "TEST-APP-001 ...")]` so TRX preserves the identity.
 Before each phase, musubix3 deletes
@@ -526,7 +543,7 @@ actually emits the named operation counter can prove the performance budget.
 Mutation evidence uses a configured command with
 `"mutationReport":{"format":"musubix-mutation-json","path":"..."}`. Each fresh
 schema-v1 mutant record carries a deterministic `MUT-<hash>` identity (derivable
-with the exported `mutationIdentity` helper), must-functional requirement ID,
+with the `mutationIdentity` helper exported from `musubix3/analysis`), must-functional requirement ID,
 authoritative test ID, source/test paths and SHA-256 fingerprints, operator,
 one-based line/column, and `killed|survived|skipped|error` status. The gate adds
 command, rendered-argument, report, process, and exit provenance to
@@ -535,9 +552,11 @@ with a current linked killed mutant. Duplicate/conflicting, non-killed, stale,
 unlinked, altered-report, and configuration-drift evidence is rejected.
 `mutation.mode` defaults to `compatible` (absence is allowed); set it to
 `strict` and protect it plus the mutation command in the policy baseline for
-release. No mutation engine dependency is bundled. Mutation and model-
-correspondence semantic heads are included in attestations and their underlying
-provenance is revalidated.
+release. No mutation engine dependency is bundled. For Python, `mutation doctor`
+recommends removing existing `__pycache__` directories before each run, then
+using `python -B -m mutmut` and `python -B -m pytest` to avoid new bytecode. Mutation and model-correspondence
+semantic heads are included in attestations and their underlying provenance is
+revalidated.
 
 Quality evidence records required flags, actual exits/output, metrics,
 timestamps and input fingerprints. Changed-run paths, HEAD and impacts survive a
@@ -558,12 +577,23 @@ hash and canonical transcript hash are persisted. `workflow.expectedSessionId`
 or `--session-id` rejects substitution with a different caller-declared session.
 Strict verification also bounds terminal transcript age and future clock skew
 with `workflow.maxAgeSeconds` and `workflow.maxFutureSkewSeconds`.
-Unrelated concurrent events may be emitted out of timestamp order, so strict mode
-checks causal tool/result ordering rather than imposing a global timestamp sort.
+Unrelated concurrent events—and even timestamps produced by different execution
+clocks—may be non-monotonic, so strict mode uses JSONL source order for causal
+tool/result lifecycles rather than imposing a timestamp sort. Pair/terminal clock
+skew is enforced only when `maxEventSkewMs` is explicitly supplied; terminal age
+and future-skew policies remain independently enforced. Verification remains
+streaming and resource-bounded: transcripts default to 100,000,000 bytes, while
+`workflow.maxTranscriptBytes` can explicitly raise the limit up to 1,000,000,000
+bytes. Individual JSONL records default to 1,000,000 bytes and can be bounded up
+to 10,000,000 with `workflow.maxTranscriptLineBytes`. Protect both chosen bounds
+in the policy baseline so they cannot be widened silently.
 If project inputs change while a gate is running, `input-stability` reports each
 added, modified, or deleted path with before/after SHA-256 values. Standard
 Cargo/Maven `target/`, manifest-scoped .NET `bin/` and `obj/`, and project-local
 `.nuget/packages/` output are excluded, but source-like generated inputs remain fail-closed.
+Write command-generated reports under `.musubix/evidence/native/` rather than the
+tracked source tree, otherwise a command that writes its own report during the
+gate invalidates input stability.
 Built-in adapters own their targeting and report arguments. A
 legacy leading Cargo/Go `test` subcommand is merged safely; conflicting report
 flags such as `--json-report` are rejected.

package/dist/packages/analysis/src/adapters.js

@@ -206,10 +206,11 @@ function status(value) {
     return 'failed';
 }
 function unique(tests) {
+    const severity = { passed: 0, skipped: 1, failed: 2, error: 3 };
     const byId = new Map();
     for (const test of tests) {
         const previous = byId.get(test.id);
-        if (!previous || previous.status === 'skipped' || test.status === 'error' || test.status === 'failed')
+        if (!previous || severity[test.status] > severity[previous.status])
             byId.set(test.id, test);
     }
     return { schemaVersion: 1, tests: [...byId.values()].sort((a, b) => a.id.localeCompare(b.id)) };
@@ -354,8 +355,10 @@ export function normalizeAdapterReport(adapter, text, targetTestId) {
         tests.push(...dotnetResults(text));
     }
     else {
-        for (const match of text.matchAll(/<testcase\b([^>]*)>([\s\S]*?)<\/testcase>|<testcase\b([^>]*)\/>/g)) {
-            const attributes = match[1] ?? match[3] ?? '';
+        const attributeText = '(?:[^>"\']|"[^"]*"|\'[^\']*\')*?';
+        const testcase = new RegExp(`<testcase\\b(${attributeText})(?:/>|>([\\s\\S]*?)</testcase>)`, 'g');
+        for (const match of text.matchAll(testcase)) {
+            const attributes = match[1] ?? '';
             const body = match[2] ?? '';
             const identityText = /\bname="([^"]*)"/.exec(attributes)?.[1]
                 ?? /\bclassname="([^"]*)"/.exec(attributes)?.[1];

package/dist/packages/analysis/src/adapters.js.map

@@ -1 +1 @@
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package/dist/packages/analysis/src/config.d.ts

@@ -56,6 +56,8 @@ export interface WorkflowConfig {
     maxAgeSeconds?: number;
     maxFutureSkewSeconds?: number;
     maxEventSkewMs?: number;
+    maxTranscriptBytes?: number;
+    maxTranscriptLineBytes?: number;
 }
 export interface CodeGraphConfig {
     mode: 'compatible' | 'strict';

package/dist/packages/analysis/src/config.js

@@ -13,7 +13,7 @@ export const defaultConfig = {
     formal: { solver: 'none', minModeledFraction: 0, timeoutMs: 12_000 },
     mutation: { mode: 'compatible' },
     tdd: { redPreflightCommands: [] },
-    workflow: { mode: 'compatible', maxAgeSeconds: 3600, maxFutureSkewSeconds: 60, maxEventSkewMs: 1000 },
+    workflow: { mode: 'compatible', maxAgeSeconds: 3600, maxFutureSkewSeconds: 60 },
     attestation: {
         mode: 'local',
         maxAgeSeconds: 3600,
@@ -275,7 +275,7 @@ export function parseConfig(input) {
         throw new Error('mutation.mode must be compatible or strict.');
     }
     const rawWorkflow = object(optional(value.workflow, {}), 'workflow');
-    keys(rawWorkflow, ['mode', 'expectedSessionId', 'maxAgeSeconds', 'maxFutureSkewSeconds', 'maxEventSkewMs'], 'workflow');
+    keys(rawWorkflow, ['mode', 'expectedSessionId', 'maxAgeSeconds', 'maxFutureSkewSeconds', 'maxEventSkewMs', 'maxTranscriptBytes', 'maxTranscriptLineBytes'], 'workflow');
     const workflowMode = optional(rawWorkflow.mode, defaultConfig.workflow.mode);
     if (!['compatible', 'strict'].includes(String(workflowMode))) {
         throw new Error('workflow.mode must be compatible or strict.');
@@ -299,10 +299,23 @@ export function parseConfig(input) {
         throw new Error('workflow.maxFutureSkewSeconds must be 0..600.');
     }
     const workflowMaxEventSkewMs = optional(rawWorkflow.maxEventSkewMs, defaultConfig.workflow.maxEventSkewMs);
-    if (typeof workflowMaxEventSkewMs !== 'number' || !Number.isInteger(workflowMaxEventSkewMs)
-        || workflowMaxEventSkewMs < 0 || workflowMaxEventSkewMs > 60_000) {
+    if (workflowMaxEventSkewMs !== undefined
+        && (typeof workflowMaxEventSkewMs !== 'number' || !Number.isInteger(workflowMaxEventSkewMs)
+            || workflowMaxEventSkewMs < 0 || workflowMaxEventSkewMs > 60_000)) {
         throw new Error('workflow.maxEventSkewMs must be 0..60000.');
     }
+    const workflowMaxTranscriptBytes = optional(rawWorkflow.maxTranscriptBytes, defaultConfig.workflow.maxTranscriptBytes);
+    if (workflowMaxTranscriptBytes !== undefined
+        && (typeof workflowMaxTranscriptBytes !== 'number' || !Number.isSafeInteger(workflowMaxTranscriptBytes)
+            || workflowMaxTranscriptBytes < 1 || workflowMaxTranscriptBytes > 1_000_000_000)) {
+        throw new Error('workflow.maxTranscriptBytes must be 1..1000000000.');
+    }
+    const workflowMaxTranscriptLineBytes = optional(rawWorkflow.maxTranscriptLineBytes, defaultConfig.workflow.maxTranscriptLineBytes);
+    if (workflowMaxTranscriptLineBytes !== undefined
+        && (typeof workflowMaxTranscriptLineBytes !== 'number' || !Number.isSafeInteger(workflowMaxTranscriptLineBytes)
+            || workflowMaxTranscriptLineBytes < 1 || workflowMaxTranscriptLineBytes > 10_000_000)) {
+        throw new Error('workflow.maxTranscriptLineBytes must be 1..10000000.');
+    }
     const rawAttestation = object(optional(value.attestation, {}), 'attestation');
     keys(rawAttestation, [
         'mode', 'repository', 'maxAgeSeconds', 'maxFutureSkewSeconds', 'trustedPublicKeys', 'githubOidc',
@@ -386,7 +399,9 @@ export function parseConfig(input) {
             ...(typeof rawWorkflow.expectedSessionId === 'string' ? { expectedSessionId: rawWorkflow.expectedSessionId } : {}),
             maxAgeSeconds: workflowMaxAgeSeconds,
             maxFutureSkewSeconds: workflowMaxFutureSkewSeconds,
-            maxEventSkewMs: workflowMaxEventSkewMs,
+            ...(workflowMaxEventSkewMs === undefined ? {} : { maxEventSkewMs: workflowMaxEventSkewMs }),
+            ...(workflowMaxTranscriptBytes === undefined ? {} : { maxTranscriptBytes: workflowMaxTranscriptBytes }),
+            ...(workflowMaxTranscriptLineBytes === undefined ? {} : { maxTranscriptLineBytes: workflowMaxTranscriptLineBytes }),
         },
         attestation: {
             mode: mode,
@@ -503,6 +518,16 @@ export function policyDiagnostics(config, baseline, changed = null) {
             diagnostics.push(error('POLICY_TDD_PREFLIGHT', `TDD Red preflight command ${command} differs from the trusted baseline definition.`));
         }
     }
+    const configuredTranscriptBytes = config.workflow.maxTranscriptBytes ?? 100_000_000;
+    const baselineTranscriptBytes = baseline.workflow.maxTranscriptBytes ?? 100_000_000;
+    if (configuredTranscriptBytes > baselineTranscriptBytes) {
+        diagnostics.push(error('POLICY_WORKFLOW_TRANSCRIPT_SIZE', 'workflow.maxTranscriptBytes is weaker than the trusted baseline.'));
+    }
+    const configuredTranscriptLineBytes = config.workflow.maxTranscriptLineBytes ?? 1_000_000;
+    const baselineTranscriptLineBytes = baseline.workflow.maxTranscriptLineBytes ?? 1_000_000;
+    if (configuredTranscriptLineBytes > baselineTranscriptLineBytes) {
+        diagnostics.push(error('POLICY_WORKFLOW_TRANSCRIPT_LINE_SIZE', 'workflow.maxTranscriptLineBytes is weaker than the trusted baseline.'));
+    }
     if (baseline.workflow.mode === 'strict') {
         if (config.workflow.mode !== 'strict') {
             diagnostics.push(error('POLICY_WORKFLOW_MODE', 'workflow.mode cannot be weakened below strict as required by the trusted baseline.'));
@@ -517,7 +542,9 @@ export function policyDiagnostics(config, baseline, changed = null) {
         if ((config.workflow.maxFutureSkewSeconds ?? 60) > (baseline.workflow.maxFutureSkewSeconds ?? 60)) {
             diagnostics.push(error('POLICY_WORKFLOW_FUTURE_SKEW', 'workflow.maxFutureSkewSeconds is weaker than the trusted baseline.'));
         }
-        if ((config.workflow.maxEventSkewMs ?? 1000) > (baseline.workflow.maxEventSkewMs ?? 1000)) {
+        const configuredEventSkew = config.workflow.maxEventSkewMs ?? Number.POSITIVE_INFINITY;
+        const baselineEventSkew = baseline.workflow.maxEventSkewMs ?? Number.POSITIVE_INFINITY;
+        if (configuredEventSkew > baselineEventSkew) {
             diagnostics.push(error('POLICY_WORKFLOW_EVENT_SKEW', 'workflow.maxEventSkewMs is weaker than the trusted baseline.'));
         }
     }